R: Estimation and assessment of raw copy numbers at the single...

doCRMAv1 {aroma.affymetrix}

R Documentation

Estimation and assessment of raw copy numbers at the single locus level (CRMA v1)

Description

Estimation and assessment of raw copy numbers at the single locus level (CRMA v1) based on [1]. The algorithm is processed in bounded memory, meaning virtually any number of arrays can be analyzed on also very limited computer systems.

Usage

  ## S3 method for class 'AffymetrixCelSet'
doCRMAv1(csR, shift=+300, combineAlleles=TRUE, lengthRange=NULL, arrays=NULL, drop=TRUE,
  verbose=FALSE, ...)
  ## Default S3 method:
doCRMAv1(dataSet, ..., verbose=FALSE)
  ## Default S3 method:
doASCRMAv1(...)

Arguments

`csR`, `dataSet`	An `AffymetrixCelSet` (or the name of an `AffymetrixCelSet`).
`shift`	An tuning parameter specifying how much to shift the probe signals before probe summarization.
`combineAlleles`	A `logical` specifying whether allele probe pairs should be summed before modeling or not.
`lengthRange`	An optional `numeric` vector of length two passed to `FragmentLengthNormalization`.
`arrays`	A `integer` `vector` specifying the subset of arrays to process. If `NULL`, all arrays are considered.
`drop`	If `TRUE`, the summaries are returned, otherwise a named `list` of all intermediate and final results.
`verbose`	See `Verbose`.
`...`	Additional arguments used to set up `AffymetrixCelSet` (when argument `dataSet` is specified).

Value

Returns a named list, iff drop == FALSE, otherwise only ChipEffectSet object.

Allele-specific or only total-SNP signals

If you wish to obtain allele-specific estimates for SNPs, which are needed to call genotypes or infer parent-specific copy numbers, then use argument combineAlleles=FALSE. Total copy number signals are still available. If you know for certain that you will not use allele-specific estimates, you will get slightly less noisy signals (very small difference) if you use combineAlleles=TRUE.

doASCRMAv1(...) is a wrapper for doCRMAv1(..., combineAlleles=FALSE).

Author(s)

Henrik Bengtsson

References

[1] H. Bengtsson, R. Irizarry, B. Carvalho & T.P. Speed. Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics, 2008.